diff --git a/editor/editor_node.cpp b/editor/editor_node.cpp
index 2cee2c2198b0..dc902564906c 100644
--- a/editor/editor_node.cpp
+++ b/editor/editor_node.cpp
@@ -1285,7 +1285,14 @@ void EditorNode::save_resource(const Ref<Resource> &p_resource) {
 	if (p_resource->is_built_in()) {
 		const String scene_path = p_resource->get_path().get_slice("::", 0);
 		if (!scene_path.is_empty()) {
-			save_scene_if_open(scene_path);
+			if (ResourceLoader::exists(scene_path) && ResourceLoader::get_resource_type(scene_path) == "PackedScene") {
+				save_scene_if_open(scene_path);
+			} else {
+				// Not a packed scene, so save it as regular resource.
+				Ref<Resource> parent_resource = ResourceCache::get_ref(scene_path);
+				ERR_FAIL_COND_MSG(parent_resource.is_null(), "Parent resource not loaded, can't save.");
+				save_resource(parent_resource);
+			}
 			return;
 		}
 	}
diff --git a/editor/plugins/script_editor_plugin.cpp b/editor/plugins/script_editor_plugin.cpp
index 5ff8cd17eaf7..e986510895dd 100644
--- a/editor/plugins/script_editor_plugin.cpp
+++ b/editor/plugins/script_editor_plugin.cpp
@@ -1001,6 +1001,11 @@ void ScriptEditor::_res_saved_callback(const Ref<Resource> &p_res) {
 		}
 	}
 
+	if (p_res.is_valid()) {
+		// In case the Resource has built-in scripts.
+		_mark_built_in_scripts_as_saved(p_res->get_path());
+	}
+
 	_update_script_names();
 	Ref<Script> scr = p_res;
 	if (scr.is_valid()) {
@@ -1010,6 +1015,10 @@ void ScriptEditor::_res_saved_callback(const Ref<Resource> &p_res) {
 
 void ScriptEditor::_scene_saved_callback(const String &p_path) {
 	// If scene was saved, mark all built-in scripts from that scene as saved.
+	_mark_built_in_scripts_as_saved(p_path);
+}
+
+void ScriptEditor::_mark_built_in_scripts_as_saved(const String &p_parent_path) {
 	for (int i = 0; i < tab_container->get_tab_count(); i++) {
 		ScriptEditorBase *se = Object::cast_to<ScriptEditorBase>(tab_container->get_tab_control(i));
 		if (!se) {
@@ -1022,7 +1031,7 @@ void ScriptEditor::_scene_saved_callback(const String &p_path) {
 			continue; // External script, who cares.
 		}
 
-		if (edited_res->get_path().get_slice("::", 0) == p_path) {
+		if (edited_res->get_path().get_slice("::", 0) == p_parent_path) {
 			se->tag_saved_version();
 		}
 
diff --git a/editor/plugins/script_editor_plugin.h b/editor/plugins/script_editor_plugin.h
index 6d13c6af09fa..d5c33c73b4ef 100644
--- a/editor/plugins/script_editor_plugin.h
+++ b/editor/plugins/script_editor_plugin.h
@@ -401,6 +401,7 @@ class ScriptEditor : public PanelContainer {
 	void _add_callback(Object *p_obj, const String &p_function, const PackedStringArray &p_args);
 	void _res_saved_callback(const Ref<Resource> &p_res);
 	void _scene_saved_callback(const String &p_path);
+	void _mark_built_in_scripts_as_saved(const String &p_parent_path);
 
 	bool open_textfile_after_create = true;
 	bool trim_trailing_whitespace_on_save;
diff --git a/editor/plugins/shader_editor_plugin.cpp b/editor/plugins/shader_editor_plugin.cpp
index 9321c6dafc09..213a332bab76 100644
--- a/editor/plugins/shader_editor_plugin.cpp
+++ b/editor/plugins/shader_editor_plugin.cpp
@@ -625,12 +625,37 @@ void ShaderEditorPlugin::_file_removed(const String &p_removed_file) {
 	}
 }
 
+void ShaderEditorPlugin::_res_saved_callback(const Ref<Resource> &p_res) {
+	if (p_res.is_null()) {
+		return;
+	}
+	const String &path = p_res->get_path();
+
+	for (EditedShader &edited : edited_shaders) {
+		Ref<Resource> shader_res = edited.shader;
+		if (shader_res.is_null()) {
+			shader_res = edited.shader_inc;
+		}
+		ERR_FAIL_COND(shader_res.is_null());
+
+		if (!edited.shader_editor || !shader_res->is_built_in()) {
+			continue;
+		}
+
+		if (shader_res->get_path().get_slice("::", 0) == path) {
+			edited.shader_editor->tag_saved_version();
+			_update_shader_list();
+		}
+	}
+}
+
 void ShaderEditorPlugin::_notification(int p_what) {
 	switch (p_what) {
 		case NOTIFICATION_READY: {
 			EditorNode::get_singleton()->connect("resource_saved", callable_mp(this, &ShaderEditorPlugin::_resource_saved), CONNECT_DEFERRED);
 			EditorNode::get_singleton()->connect("scene_closed", callable_mp(this, &ShaderEditorPlugin::_close_builtin_shaders_from_scene));
 			FileSystemDock::get_singleton()->connect("file_removed", callable_mp(this, &ShaderEditorPlugin::_file_removed));
+			EditorNode::get_singleton()->connect("resource_saved", callable_mp(this, &ShaderEditorPlugin::_res_saved_callback));
 		} break;
 	}
 }
diff --git a/editor/plugins/shader_editor_plugin.h b/editor/plugins/shader_editor_plugin.h
index 84c5a620a722..25581849825f 100644
--- a/editor/plugins/shader_editor_plugin.h
+++ b/editor/plugins/shader_editor_plugin.h
@@ -96,6 +96,7 @@ class ShaderEditorPlugin : public EditorPlugin {
 	void _close_shader(int p_index);
 	void _close_builtin_shaders_from_scene(const String &p_scene);
 	void _file_removed(const String &p_removed_file);
+	void _res_saved_callback(const Ref<Resource> &p_res);
 
 	void _shader_created(Ref<Shader> p_shader);
 	void _shader_include_created(Ref<ShaderInclude> p_shader_inc);